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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
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        About MultiQC

        This report was generated using MultiQC, version 1.28

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the PavlidisLab/sc-annotation-pipeline analysis pipeline.
        Report generated on 2025-04-29, 13:09 PDT based on data in: /space/grp/rschwartz/rschwartz/cell_annotation_cortex.nf/hsap/31/1ab15cd13796ecbec3287a7974d42e/PTSDBrainomics

        Sample Outlier Composition (outliers)

        Sample Outlier Composition (outliers) test.

        Created with MultiQC

        Sample cell type composition

        Sample cell type composition test.

        Created with MultiQC

        Leiden Cluster Composition (outliers)

        Leiden Cluster Composition (outliers) test.

        Created with MultiQC

        Leiden cluster composition (cell types)

        Leiden cluster composition (cell types) test.

        Created with MultiQC

        Cell type markers

        Cell type markers test.

        Created with MultiQC

        Cell type markers table

        Cell type markers table test.

        Showing 37/37 rows and 4/4 columns.
        Sample Namecell_typeclassfamilymarkers
        0
        caudal ganglionic eminence derived GABAergic cortical interneuron
        CGE
        GABAergic
        NR2F2
        1
        lamp5 GABAergic cortical interneuron
        CGE
        GABAergic
        LAMP5
        2
        sncg GABAergic cortical interneuron
        CGE
        GABAergic
        SNCG
        3
        vip GABAergic cortical interneuron
        CGE
        GABAergic
        VIP
        4
        chandelier pvalb GABAergic cortical interneuron
        MGE
        GABAergic
        COL25A1
        5
        pvalb GABAergic cortical interneuron
        MGE
        GABAergic
        PVALB
        6
        sst chodl GABAergic cortical interneuron
        MGE
        GABAergic
        CHODL
        7
        sst GABAergic cortical interneuron
        MGE
        GABAergic
        SST
        8
        Cajal-Retzius cell
        Cajal-Retzius cell
        Glutamatergic
        RELN
        9
        corticothalamic-projecting glutamatergic cortical neuron
        deep layer non-IT
        Glutamatergic
        FOXP2
        10
        L5 ET neuron
        deep layer non-IT
        Glutamatergic
        FEZF2
        11
        near-projecting glutamatergic neuron
        deep layer non-IT
        Glutamatergic
        TLE4
        12
        L6 CT neuron
        deep layer non-IT
        Glutamatergic
        NTSR1
        13
        L6b neuron
        deep layer non-IT
        Glutamatergic
        TOX2
        14
        CA1-prosubiculum hippocampal neuron
        Hippocampal
        Glutamatergic
        WFS1
        15
        CA2-IG-FC hippocampal neuron
        Hippocampal
        Glutamatergic
        RGS14
        16
        CA3 hippocampal neuron
        Hippocampal
        Glutamatergic
        GRIK4
        17
        dentate gyrus hippocampal neuron
        Hippocampal
        Glutamatergic
        CALB1
        18
        subiculum hippocampal neuron
        Hippocampal
        Glutamatergic
        GRM2
        19
        L2/3 IT neuron
        L2/3-6 IT
        Glutamatergic
        CUX1
        20
        L4/5 IT neuron
        L2/3-6 IT
        Glutamatergic
        RORB
        21
        L6 Car3 neuron
        L2/3-6 IT
        Glutamatergic
        CAR3
        22
        neural stem cell
        Neuroglioblast
        Neuroglioblast
        SOX2
        23
        neuroepithelial stem cell
        Neuroglioblast
        Neuroglioblast
        PAX6
        24
        CNS macrophage
        CNS macrophage
        Non-neuron
        CD68
        25
        microglial cell
        CNS macrophage
        Non-neuron
        TMEM119
        26
        astrocyte
        Glia
        Non-neuron
        GFAP
        27
        ependymal cell
        Glia
        Non-neuron
        FOXJ1
        28
        oligodendrocyte
        Glia
        Non-neuron
        MOG
        29
        OPC
        Glia
        Non-neuron
        PDGFRA
        30
        CD8+ T cell
        Immune
        Non-neuron
        CD8A
        31
        NK T cell
        Immune
        Non-neuron
        NKG7
        32
        T cell
        Immune
        Non-neuron
        TRAC
        33
        pericyte
        Mural
        Non-neuron
        RGS5
        34
        smooth muscle cell
        Mural
        Non-neuron
        MYH11
        35
        leptomeningeal cell
        Stromal
        Non-neuron
        LUM
        36
        endothelial cell
        Vascular
        Non-neuron
        VWF

        PTSDBrainomics | sc12 combined

        PTSDBrainomics | sc13 combined

        PTSDBrainomics | sc11 combined

        PTSDBrainomics | sc5 combined

        PTSDBrainomics | sc18 combined

        PTSDBrainomics | sc33 combined

        PTSDBrainomics | sc44 combined

        PTSDBrainomics | sc32 combined

        PTSDBrainomics | sc31 combined

        PTSDBrainomics | sc7 combined

        PTSDBrainomics | sc6 combined

        PTSDBrainomics | sc1 combined

        PTSDBrainomics | sc34 combined

        PTSDBrainomics | sc21 combined

        PTSDBrainomics | sc2 combined

        PTSDBrainomics | sc42 combined

        PTSDBrainomics | sc35 combined

        PTSDBrainomics | sc3 combined

        PTSDBrainomics | sc43 combined

        MultiQC v1.28 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap and FileSaver.js.